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ECE410-ECENeuroScience-F22

ECE-410/NE-410 Weekly Schedule Fall 2022

Part I: Lectures, Past Videos, Reading assignments: Calendar Weeks 34-37
WeekMWF
34L1: Read: \(\ \S \) 1.1 (Preface: pp vii-x; Ch 1: History pp 1-8);
2021 360 Lec 1 (Starts @6:00 mins)
L2: Read: \( \S \) 1.2 (p. 8-11); F22 Aug 24, Lec 2;
2021 360 Lec 2 (Starts @14:00 mins)
L3: Read: \( \S \) 1.3 (p. 11-19); \(\S\) 9.1 p. 187-104; F22 Aug 26; Lec 3;
2021 360 Lec 3
35L4: Read:Scott Ch. 12, \( \S \) 12.1 (p. 293-298); F22 L4 @5:30
Network Postulates
Assignment: NS1: Due by Lec 11; (NS1.pdf, pp. 150-151
Allen (2020); Solution: (NS1-sol.pdf);
2021 360: Lec 4
L5: Read: 2.1, .2 (p. 25-31, 189, 208); F22 Aug 31 @ 1:40;
Generic neurons (Scott: Fig. 2.1);
2021 360: Lec 5 (@2:15m)
L6: Read: 2.2.2-.3 (p. 31-35) Nonlinear Diffusion lines (LTSpice):
F22, Lec6 @ 8:00 min
36Labor DayL7: Read: \(\S\) 2.3 (p. 35-40) Synapses & Gap junction;
2021 360 Lec 7 (@1:00m)
L8: Read: \(\S\) 10-.1.2 AI models: (pp. 233-241), Neural Boolean Hilbert-space;
Discuss how solve NS1 problems;
2021 360 Lec 8 (@4:00 m)
37L9: Read: \(\S\) 10.2 (p. 241-248),
2021 360Lec 9 (@0:37m)
  
L/WDDateDaily lectures
    Part I: Introduction and History
1/34M8/22L1: Introduction to Neuroscience for engineers; The role of H. von Helmholtz; Younger years, Dynamics of a Nerve Impulse,; von Helmholtz; history,
Virtual Rat:, computational models;
Thermodynamics of the Lungs (hypertension): SpO2, CO2 and O2 lung transport models + Basics; A piece of thermodynamic history; Heart Rate vs Mortality Source of Hypertension; Theory of Hypertension; Arterial Pressure model
2W8/24L2: The structure of a nerve cell Brain anatomy; Body, Neuron Glia, DNA and Genetics, Quanta Magazine articles, #1
3/F8/26L3: Dendritic trees \(\S\) 9.0, p. 187; Organization of the brain; Numbers and density of neurons in the human brain (p. 274); McCullochPitts.43.pdf;
AI and brain waves; The making a brain map
4/35M8/29L4: The Hierarchical Nature of Brain Dynamics; Integration of the 5 main sensory inputs; Brain fumction and integration Orexin & the Theory of weight gain/loss
Assignment: NS1: Matlab homework on the diffusion and wave equations. Due by Lec 11; (pdf), Postulates
For a discussion of the solution method look at Book; \(\S\) 4.8.3 (pp. 143-147). A detailed example is discussed on pages 149-151;
5W8/31L5: The generic neuron; Action potentials; Voltage-gated membrane channels; Neuron, Body
Σ-∆ codec, png
6F9/2L6: Nonlinear diffusion model General solution ;NL-RC Neural Spike model (.cir); , using spice [.asc]; Input & Mylin Voltages
The nonlinear diffusion line and why it acts as a delay line, Diode circuit model of spike propagation, Results from circuit model
Results of LT spice model from William Walters (HW6 4/6/21)
Leading edge models: Chap. 5, p. 95;
NGspice users manual (pdf)
-/36M9/5Labor Day (Holiday)
7W9/7L7: Chemical synapse, gap junction, Synapse, Neuron, types of Neurotransmitters;
8F9/9L8: McCulloch-Pitts (MP) AI neuron (model), (M-P model; pdf); \(\S\) 10.1.1-.2: (pp. 235-241) Boolean Hilbert space;
Dendritic Boolean logic (i.e., processing);Generalized scalar products (Allen book \( \S \) 3.5.1, Fig 3.4); Just how smart is AI?; AI-Transformers, Basic brain anatomy, (pdf)
How do AI models work?; Deep-learning
Real neural networks; Water (Life?) on Mars (@7:02); The beginning of live on earth
9/37M9/12L9: Deep-learning concepts: STFT and fast convolution; ConvNetJS discussion, Sejnowski.20.pdf
Discuss solution to trainmission problem
Assignment: NS2 (pdf, (sol), Gscope, Due by Lec 14

Part II: Lectures, Videos, Reading assignments + videos: Calendar Weeks 37-41
WeekMWF
37 L10: Read: \( \S \) 3, 3.1 (p. 49-53) 360 Lec10L11: Read: \( \S \) 3.2 (p. 53-55) Solution: (NS1-sol.pdf) 360 Lec 11
38L12: Read: \( \S \) 3.3 (p. 56-57) 360 Lec 12 (@1:25 min)L13: Read: \( \S \) 3.3.3 (p. 58-60) 360 Lec 13 (Starts @ 2:30 12:19--13:19)L14: ''Read: \( \S \) 3.4 (p. 60-63) Membrane models 360 Lec 14 (@1:30); NS2 due; (sol)
39L15: Exam I L16: Read: \( \S \) 3.5 (p. 63-65) Na & K pumps and Nernst potentials Lec16 (@3:00)
L17: Read: \( \S \) 4.1, (p. 67-69) 360 Lec 17
40L18: Read: \( \S \) 4.1-4.2 (p. 70-74) 360 Lec 18L19: Read: \( \S \) 4.3 (p. 74-77)
L20: Read: \( \S \) 4.4, 4.5 (p. 77-80) Lec 20 F20 @0:47;
41L21: Read: \( \S \) 3.4, 4.5.2, 4.6, (p. 80-87) Figs 4.5-4.8 360 L21L22: Read: \(\S\) 4.7 Matlab similink Diode model NS3 dueL23:Read: §10 (p. 233-241); Review sol to NS3;
L/WDDateDaily lectures
    Part II: Structure of a Neuron
10/37W9/14L10: Lipid bilayers and their electro/mechanical properties Allen Lec 11, 2021; Allen Lec 10, 2022; Lipid bilayers, Transport mechanisms, Fun with bubbles, AI and protein folding
11F9/16L11: Electrochemical properties of membranes; hemoglobum and oxyen transport; Hill function
See A.V. Hill Equation in biochemistry;
Blue whale's heart rate
Assignment: NS1 due, Solution: (NS1-sol.pdf)
12/38M9/19L12: Transmembrane currents; Channels & types; Calculating partial pressures (It is an impedance calculation.)
13W9/21L13: Einstein's relation (1905-II) and its derivation Einstein's 4 papers in 1905 Basic Solutions, Numerical solutions;
System Postulates.pdf
14F9/23L14: Review for Exam I NS2 Due; NS2 Solution
15/39M9/26L15: --NO CLASS-- Exam I: 3--5 PM Rm. 2017 ECEB Next year:Move Exam I to Lec 23;
Compress/combine/reduce Lec 16-22; More on brain Assemblies (Ch 11); eye & ear & touch transduction
16W9/28L16: Ionic currents (conduction, diffusion currents), electrochemistry
Assignment: NS3 pdf, Due by Lec 22 NS3 Solution
17F9/30L17: Redox Resting potentials and pumps HH matlab model; Helmholtz measures velocity of spikes
18/40M10/3L18: Ch. 4,Hodgkin Huxley model: U Mich.s; Fine-tuning the HH model to work off the spike rising onset; HH model (matlab code);
Ion distribution during a spike; Neural oscillators
19W10/5L19: Squid Voltage patch clamp for single cell recording; Adrian and nerve pulses first neural recording from toad eye (1928)
20F10/7L20:Critical point in nonlinear diffusion (cable) equation Muscle dynamics, Neurological disorders, Guillain-Barre syndrom, Demylination disorders; Talk on neural regeneration Jan 25, NSP
21/41M10/10L21: Nodes of Ranvier; Krebs cycle as the energy source; Mitochondrion
22W10/12L22: Read:\(\S\)9.1 (187-199, Fig. 9.1) Spike models @3m; Myelin-Sheath @11m; Information processing: \(\S\)9--9.2: @33:40m; @49 bifurcations;
23F10/14L23: Review sols NS3, Read: \(\S\)10 (p. 233-241); 360 Lec 25 @2:25; topic II: @38:25 NS3 due, NS3 Solution
Part III: Lectures, Videos, Reading assignments + videos: Calendar Weeks 12-17
WeekMWF
42L24: 360 Lec 26 (@1);
Read: Donald Hebb \(\S\)11 (pp. 17-19);
L25: (360 L27 @3:00);Read: Cell-Assembly, \( \S \) 11-.3 (pp. 257-265) of word frequencies;
L26: Cell-Assembly and language hypothesis;
43L27: Zipf's log-linear Law; Brief review for Exam II
L28: Exam II
L29: (360 L28 A(@0:48); B(@11:30);
Read: \( \S \) 10-10.1.1 (233-237), 11-11.2 (256-265)
44L30: Hypertension and its source: 360 L29 (@0)
Read: \( \S \) 9.3.2, 10.1.2, 11.3: Dendritic Boolean logic
L31: L30-360 (2021); Mayfield Brain Anatomy (pdf); cortex anatomy
Read: \( \S \) 10.2.2 (241-248)
L32: Molecular Transport; Protein creation;
L34-360: (2021): Discovery of DNA and RNA;
L33-360: (2022) Thalamus, L32-360: (2021) (@0:25), Hippocampus,
L31-360: (2021) (@4:25) Topic: Brain anatomy;
Read: \( \S \) 9.3, 10.3 (248-252)
45L33: L35-360 S21: The eyes and ears (@3:15m)
Ch 5: Frog vision;
L34: Overview of Sensory systems (Hearing)
L36-360 S21: Hearing (@1:00),
L35: L37-360: Cochlear Transduction
46L36: The inner ear and its function; Cochlear nonlinear processing (@2min),
NL Cochlear processing (pdf), Ashmore Lecture
L37: Organ of CortiL38: Cochlear nonlinearities and its function
-/47S11/19 Fall Break
48L39: Sensory systems; Vrius; Crisper (360 S21: Audio starts @ 22m)
Read: \( \S \) 8.0-8.3 (165-169));
L40: 360 S21 (@1m)
AI's furure, AI darkside; Conscious;
Short term memory
Assignment: NS7 Due
L41: Amy Arnsten: Excutive Control, Abstract reasoning in the PreFrontalCortex
49L42: Koch on consciousness (@1:13), Giulio Tononi on Consciousness
L43 Review for final exam (Disc relevant and possible topics)Thur: Reading Day;
L/WDDateDaily Lectures
    Part III: Neuronal & Cell Assemblies
24/42M10/17L24: Information processing; Dendritic information processing; Dendritic logic processing (Ch 9; State machines & Branching rules in dendrites); Cell assemblies: Recent Evidence; gap junction disorders, proteins; EM micrographs
Synaptic processing videos: Neural computation power, How brains learn, How networks learn: (Audio podcast 163): (no video) @1:00; Synaptic Information processing (Audio podcast 148): @0:16 (no video),
Backpropagation Methods for machine learning:; Hinton's BackProb Training algorithm;
Assignment: Due by Lec 28; (NS4.pdf; NS4-sol.pdf)
25W10/19L25: (-->L27) Energy sources; mitrohcondrial membrane; Rebooting how cells remember structure: Levin lecture @4:39m; Levin: New Yorker article on his regeneration research:
26F10/21L26: (-->L25) Early Evidence for Cell Assemblies (Hebb) Neural Syntax: Realizations of Hebb's Cell Assemblies: Language Hypothesis; Brain facts
27/43M10/24L27: (-->L26) Zipf-Model, MaxEnt-model; Zipf's log-linear and the Brown Corpus; Zipf's word Brevity-law Raven IQ test
28W10/26L28: Exam II: NS3, NS4, Historical events
29F10/28L29: L29: Hyppocampus and memory; Neurosurgry of the brain; Spatial orientation,
Measures of inntelligence (IQ): Raven's Progressive Matricies
Mental images; Induced love between mice Limbic System
Assignment: NS5, Due on L32 (pdf, NS5-sol)
30/44M10/31L30 Role of vital signs: How the heart rate is regulated by the body (video), Heart Rate vs Mortality, Source of Hypertension,
Kosinski-Theory of Hypertension-I (2018), Kosinski-Theory of Hypertension-II (2018), Arterial Pressure model; VirtualRat Model: Vital signs Model (pdf)
31W11/2L31: A:Brain Anatomy; B:Field Theories for the Neocortex \(\S 9.3\); Models of Brain Anatomy (Dynamics I-II)
Zidovska Life of Cell Nucleus; Friston Predictive model, claustrum Limits of brain and muscle; Senses of Orientation (NIH); Allen Inst: 12 easy pieces: sentory systems; Allen Inst Brain Atlas;
Allen Inst Home Page; Start @ 6 min; Lung alternatives;, Where does thirst come from? The Chinese room argument
32F11/4L32: Molecular transport: Drew Barry: DNA replication, comments, RNA information processing video Momecular motors: Now they work,
Switching attention in the brain: Central manimpulation of DNA to enhance memory Michael Halassa: Thalamic Switching, Michael Halassa: Talk @ Allen Inst;
Rubisco: The enzime for life;The makeup of a virus: vurlient DNA, What is a virus;
33/45M11/7L33: Elements of sensory systems:Psychophysics of sound; Associative Network; Thought Koch: Information processing; Neuromorphic computing,
Assignment: NS6 due on Lec 37 (pdf); NS5 Due
34W11/9L34: Overview on hearing: Speech and hearing science: Loudness and its JND; Sense of Touch and Heat; electronic odor (smell) sensors;
Jeremy Nathans: A complex speech task explained'; Fungi that explodes ants; Metathesis molecular metathesis synthesis
35F11/11L35: Topics on hearing: Speech and hearing science: The middle ear: Window to hearing ;
Effects of Negative Middle Ear Pressure on Wideband Acoustic Immittance in Normal-Hearing Adults, pdf
Otitis Media & hearing loss
36/46M11/14L36: Topics on hearing: Speech and hearing science: The inner ear (cochlea); Cochlear modeling,
37W11/16L37: Auditory systems: the organ of Corti, hair cell transduction, Allen (1980) "Cochlear micromechanics: A physical model of transduction"; Fahey & Allen 1985 (pdf);
Mouse auditory brain map, How we can see with our ears., Speech Development in infants; An example of auditiory (neural) signal processing
38F11/18L38: Topics on hearing: Cochlear nonlinear in the auditory nerve: Transduction & the Organ of Corti, brain map & meaning; circuit1, circuit2, SigmaDelta
-/47   Fall Break (week 47)
39/48M11/28L39: Virus, bacteria, antibodies, bacteriophages, organoids, and CRISPER (phage, Parasites, Organoids, CRISPER, New studies re weight loss
Assignment: NS6 Due (Octave code that implements spike propagation)
40W11/30L40: Allen speech feature research: Techniques and implications (e.g., cell assemblies) for speech recognition and Machine Learning,
The failure of the perceptron; Live demo of Apple iPhone Speech recognition
41F12/2L41: Amy Arnsten: Excutive Control, Abstract reasoning in the PreFrontalCortex
42/49M12/5L42: Koch on consciousness (@1:13), Giulio Tononi on Consciousness
A final thought on threating PFAS's: The solution: DMSO is easily absorbed through the skin, taking with it complex molecules. Thus DMSO can be highly toxic!
43W12/7L43: Review for Final Exam (HWs)

L/WDDate 
-/18W12/8 Instruction Ends
-/18R12/9 Reading Day
-/19T  Final Exam: Time/Location/
 (Official Schedule)||

 ||- || F || 5/?? ||  Backup: Exam III TBD+ PM on HW1-HW11atest>><<

L= Lecture #
T= Topic #
W=week of the year, starting from Jan 1
D=day: T is Tue, W Wed, R Thur, S Sat, etc.
Each exam (I, II and Final paper) will count as 30% of your final grade, while the Assignments (NS1-DE3) plus class participation (Prof's Discussion), count for 10%. Please return the final paper by the end of the exam period.


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